After defeats to Croatia and Spain in their first two games, goals by Burak Yilmaz and Ozan Tufan gave the rejuvenated Turks hope, although they need results to go their way when the group stage concludes on Wednesday.
Should they go through, Turkey will face either Wales in Paris or hosts France in Lyon. The Czechs, however, will definitely go home, having finished bottom of the group with one point from three matches.
The Turks opened the scoring in the 10th minute when Arda Turan sent Emre Mor scampering away down the right before he crossed for Burak Yilmaz, who ghosted in to send a simple first-time shot from close range flying past Petr Cech.
The Czechs almost levelled soon afterwards when Borek Dockal headed against the foot of the post and Tomas Necid could not reach the rebound, before the latter awkwardly volleyed another good chance over 10 minutes later.
Although Turkey looked a lot more resilient than they had in their opening two games, they were on the back foot for much of the first half and the Czechs had plenty of chances to score.
Full back Pavel Kaderabek missed two great opportunities, firing a shot that Turkey keeper Volkan Babacan saved with his foot before the defender blazed wide following a slick attack down the right.
Babacan also pushed a stinging shot from Jaroslav Plasil wide as the Czechs started to find some space on the flanks.
Turkey came out all guns blazing in the second half and Emre Mor could have put them two up as he picked up a long ball and drifted in from the right before clipping a shot just over.
Yet seconds later Babacan had to make another smart save at the other end from Vladimir Darida.
Moments after Turkey were raging at an offside call that went against them, Ozan Tufan sent thousands of Turkish fans into ecstasy as Mehmet Topal teed him up to smash an unstoppable shot into the top corner from a tight angle.
The goal was greeted by a half-dozen flares lighting up the Turkish end of the ground, with some being thrown onto the pitch during the ear-splitting celebrations.
Their spirits lifted by the goal, the Turks battled for every ball in a superb defensive effort, never letting the Czechs settle as they weathered the storm to hold on for a precious victory.